Sergio Leone’s “Once Upon a Time in America,” arriving on Blu-ray today, is one of the best movies of its era, and well as having one of the most tortured histories. This gorgeous if challenging epic about Jewish gangsters is the unlikely crowning achievement of the director of Clint Eastwood’s “Man With No Name” spaghetti western trilogy, who spent more than a decade trying to get this wildly uncommercial project made.

Featuring terrific performances by Robert DeNiro and James Woods, the film received a 15-minute standing ovation when it premiered at the 1984 Cannes Film Festival. But when it was released a few weeks later by Warner Bros.’ long-defunct boutique label The Ladd Company, the 3-hour-and-49 minute film was chopped by an hour and a half. Worse, a complex non-linear narrative weaving back and forth over five decades was rearranged in strict chronology — which had the effect of rendering the movie almost totally incoherent.

I saw this version, which quickly flopped when it opened in wide release back in 1983, as well as the long version, which had a limited theatrical release after showing at the 1984 New York Film Festival. This longer director’s cut has always circulated on home video, beginning in the VHS era. While the Blu-ray is far less muddy than the special edition DVD released by Warner in 2003 (and doesn’t awkwardly split the movie over two discs) it still doesn’t do full justice to one of the most visually magnificent films of the ’80s.

It’s likely that even if the long version had gone into wide release in the U.S. in 1983 that the film would have been embraced by the public. “Once Upon a Time in America” is a very deliberately paced (i.e., slow) film that lingers over its often stunning images and can seem baffling on a first or even second viewing. The final sequence is one of the most enigmatic ever in a mainstream American movie.

Leone and at least six other writers loosely adapted Harry Gray’s novel “The Hoods,” yielding a Chinese box of a puzzle centering on the tortured relationship between best friends Noodles and Max (played as adults by DeNiro and Woods) who meet around 1920 in Williamsburg, Brooklyn and quickly climb the ladder of organized crime.

The film, which is sprinked liberally with bawdy humor, opens in the early 1930s with Noodles and Max double-crossing each other, then shifts to the late 1960s when a middle-aged Max has been summoned back to Brooklyn after a self-imposed exile of 35 years. Following that is nearly an hour and half of flashbacks set around 1920, with the protagonists played by excellent adolescent actors.

The great, elusive love of Noodles’ life, Deborah, is played as a teenager by Jennifer Connelly in her most impressive screen debut. She is far better than Elizabeth McGovern (then near the end of her brief career as a leading actress), who at age 20 gives the film’s weakest performance as the same character, especially when called upon to play her as a middle- aged woman in the 1960s.

In the section set in the 1930s, there’s an especially disturbing scene where Noodles rapes McGovern’s Deborah in the back seat of a limousine (the driver is producer Arnon Milchan) after she announces she’s going to Hollywood to be a movie star. Noodles also brutally rapes another woman (played by Tuesday Weld) during a holdup; she ends up becoming Max’s lover and the trigger for the massive double-cross.

The film’s biggest puzzle by far is the section set in the 1960’s, which climaxes with Noodles in a positively surreal encounter. Based on the movie’s final shot, many have speculated that Leone is hinting the entire sequence is an opium-induced fantasy that Noodles has in the 1930s. I think that would explain a lot of things.

DeNiro, coming off such classics as “Taxi Driver” and “Raging Bull,” gives one of his most subtle performances as the haunted, relatively laid-back Noodles. Woods, who also appears in a 20-minute excerpt from a 1999 documentary on the disc, has never done better work than as the hot-tempered Max, a role turned down by Dustin Hoffman. Eastwood reportedly passed on supporting role as a Jimmy Hoffa-like union played by Treat Williams.

Danny Aiello is hilarious as a police captain subjected to an especially cruel prank by Noodles and Max, and there are pungent cameos by Joe Pesci and Burt Young as Mafioso who unwisely go into business with Max and Noodles.

“Once Upon a Time in America” has an especially beautiful score by Ennio Morricone, which wasn’t even submitted for Oscar consideration. Leone’s final film (he died in 1989, aged 60) received not a single nomination but even with its flaws remains one of the most haunting movies of the 1980s.

The Warner Archive Collection first 2011 offerings today include four Greta Garbo DVD debuts: Robert Z. Leonard’s “Susan Lenox: Her Rise and Fall (1931) with Clark Gable in his first starring role; Monta Bell’s “The Torrent” (1926), with Garbo billed second for the only time in America, below Ricardo Cortez; “Romance” (1930) with Lewis Stone, her first teaming with director Clarence Brown; and her swan song, George Cukor’s “Two Faced Woman” co-starring Melvyn Douglas in a remake. That leaves just one surviving Garbo title not on DVD: George Fitzmaurics’s elusive and truly weird “As You Desire Me” (1932) with Douglas and Erich von Stroheim.

WAC is also releasing today a double feature with both versions of “The White Sister” — Henry King’s 1923 silent with Lillian Gish and Ronald Colman, and the 1933 remake starring Helen Hayes and Gable.